LAMMPS (22 Oct 2020)
  using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture

units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
  1 molecules
  6 atoms with max type 1
  6 bonds with max type 1
  6 angles with max type 1
  6 dihedrals with max type 1
  0 impropers with max type 0
atom_style molecular

pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic

lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6                  extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
  1 by 2 by 2 MPI processor grid

create_atoms 0 box mol cychex 734594
Created 3072 atoms
  create_atoms CPU = 0.011 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
  create_atoms CPU = 0.000 seconds

mass 1 14.027
mass 2 16.043

pair_coeff 1 1  0.1180  3.905
pair_coeff 2 2  0.2940  3.730

bond_coeff      1  260.00 1.5260
angle_coeff     1  63.0   112.40
dihedral_coeff  1  2.0 1 3

thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.623 | 9.719 | 10.01 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0 7.5430044e+16    341.92144 7.5430044e+16 1.8707026e+17 
     100            0   -3410.6986    572.28283   -2838.4158    14603.831 
     200            0   -6109.2306    483.67771   -5625.5529    5069.1821 
     204            0   -6137.0238    483.14639   -5653.8774    4952.4081 
Loop time of 1.10481 on 4 procs for 204 steps with 3872 atoms

98.2% CPU use with 4 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
    7.54300441078755e+16  -5648.75822692028  -5653.87742448419
  Force two-norm initial, final = 8.7430661e+18 74.636845
  Force max component initial, final = 4.1468626e+18 8.6800755
  Final line search alpha, max atom move = 0.0032186736 0.02793833
  Iterations, force evaluations = 204 328

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.89902    | 0.90561    | 0.90821    |   0.4 | 81.97
Bond    | 0.029749   | 0.030411   | 0.031345   |   0.4 |  2.75
Neigh   | 0.088655   | 0.088662   | 0.088666   |   0.0 |  8.03
Comm    | 0.063187   | 0.068096   | 0.070678   |   1.1 |  6.16
Output  | 4.8304e-05 | 0.00011426 | 0.00031124 |   0.0 |  0.01
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.01191    |            |       |  1.08

Nlocal:        968.000 ave         980 max         954 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost:        6630.00 ave        6644 max        6616 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs:       193550.0 ave      195957 max      191376 min
Histogram: 2 0 0 0 0 0 0 0 1 1

Total # of neighbors = 774200
Ave neighs/atom = 199.94835
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0

velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          100   -6137.0238    483.14639   -4500.0059    5429.3513 
     100    107.18608   -5623.5468    925.13786   -3461.6193    5640.5924 
     200    119.37927    -5671.054    1050.9079   -3242.6626    7494.8637 
     300    127.21276   -5646.2809    1053.2662    -3125.143    5661.4525 
     400    133.89893   -5674.1417       1139.7     -2989.42    7206.4877 
     500    138.74889   -5679.3757     1234.644   -2843.7477    6741.4965 
     600    150.20403   -5665.0258    1211.9245   -2719.9398    6299.2406 
     700     156.0507   -5681.5445    978.62091   -2902.2989    8429.7188 
     800    160.67293   -5579.9146    1214.6749   -2511.2805    5217.5425 
     900    172.06808   -5627.6903    1118.4786    -2523.767    8995.6018 
    1000    179.82813   -5508.1617    925.22393   -2507.9521    5760.9688 
    1100    190.36338   -5536.6687    1176.6794   -2163.4405    8079.5754 
    1200    195.57864     -5508.64    1163.8098   -2088.1038      7738.58 
    1300    204.05249   -5401.8527    1219.9794   -1827.3697    6562.2311 
    1400    211.74944   -5365.2571    1326.2667   -1595.6738    9772.2773 
    1500    222.08023   -5265.4213    1418.3572   -1284.5435    6395.1161 
    1600    225.86408   -5316.5874    1288.1407   -1422.2653     10163.26 
    1700    232.35057     -5192.56    1254.0031   -1257.5297    7437.3606 
    1800    238.16652    -5199.008    1457.8824   -992.98993    9783.4089 
    1900    250.86418    -5166.917    1256.4887   -1015.7777     8635.027 
    2000    262.41293   -5088.5573    1494.6069   -566.04218    9100.8833 
    2100    268.55207   -5057.9273    1459.8499   -499.33144    10002.961 
    2200    279.96891   -4963.9376    1526.8577   -206.59825    8943.2443 
    2300    286.55635   -5047.2961    1538.5334   -202.27038    10711.176 
    2400    292.56468   -4910.7083    1625.6283    90.740663    8482.6522 
    2500    297.79426   -4928.7403    1686.5107    193.93377    11481.089 
Loop time of 5.954 on 4 procs for 2500 steps with 3872 atoms

Performance: 36.278 ns/day, 0.662 hours/ns, 419.886 timesteps/s
95.5% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.4642     | 4.6298     | 4.8946     |   7.5 | 77.76
Bond    | 0.18992    | 0.19849    | 0.20566    |   1.3 |  3.33
Neigh   | 0.18926    | 0.18928    | 0.18929    |   0.0 |  3.18
Comm    | 0.56456    | 0.82727    | 1.0096     |  17.9 | 13.89
Output  | 0.00044023 | 0.00092791 | 0.0020343  |   0.0 |  0.02
Modify  | 0.077974   | 0.080378   | 0.082874   |   0.8 |  1.35
Other   |            | 0.02782    |            |       |  0.47

Nlocal:        968.000 ave         989 max         944 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost:        6381.50 ave        6416 max        6351 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs:       192557.0 ave      197456 max      188754 min
Histogram: 2 0 0 0 0 0 0 1 0 1

Total # of neighbors = 770229
Ave neighs/atom = 198.92278
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
write_data molecular-mix.data
System init for write_data ...
Total wall time: 0:00:07
